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In endemic areas, the genetic diversity among co-circulating dengue virus (DENV) strains is considerable and new, highly divergent strains are identified on a regular basis. It is thus critical to ensure that molecular diagnostic tools effectively detect virus genomes even in case of important genetic variation. Here, we tested both the pan-DENV detection capacity and the limit of detection of two real-time RT-PCR assays: (i) the commercial RealStar Altona 3.0 system and (ii) a laboratory developed test (LDT) combining two RT-PCR systems in a single reaction tube (DenAllDUO). We used a panel of DENV strains representative of the genetic diversity within DENV species, combined with three in vitro transcribed RNAs as surrogates for unavailable strains corresponding to recently discovered strains with substantial genetic divergence: DENV serotype 1 (DENV-1) Brun2014, DENV-2 QML22 and DENV-4 DKE121. Both systems (i) targeted the genome 3′ untranslated region, (ii) displayed a broad detection spectrum, encompassing most of DENV species diversity, and (iii) detected the three aforementioned divergent strains. DenAllDUO detected all the strains tested, whereas the RealStar system failed to detect strains from DENV-4 genotype III. Altogether, our findings support the value of these two RT-PCR systems as part of the Dengue diagnostic arsenal.

Feline nasal lymphoma is generally a localized radiosensitive tumor. Treatment options include radiation therapy, chemotherapy, or a combination of both modalities. Radiation therapy (RT) in a combination with chemotherapy lead to median survival from 19 months to 955 days. The objective of this paper is to report a case of a large cell late stage invasive feline nasal lymphoma and to evaluate the results of orthovoltage radiation therapy and its side effects. A 12-year-old female mixed breed cat was presented with nasal discharge, sneezing and hyporexia. Definitive histopathology diagnosis was diffuse large cell lymphoma. Computed tomography revealed an advanced stage of the disease, an intranasal mass, bone lysis, invasion of the orbital space and central nervous system. A radical course of X-ray therapy was performed (SFD = 4 Gy, TSD = 40 Gy, 10 sessions, 3 times a week). Radiation side effects were well tolerated and resolved with supportive treatment. Lymphoma is a systemic process and requires a multidisciplinary approach. On most cases, the penetrating ability of radiation therapy of 3.5 cm in depth is enough for small domestic animals. A significant effect is noted in the middle of the treatment course. The fractionated regime did not cause early radiation damage. The relapse-free period was up to 8 months. The patient had a satisfying quality of life for 5 months. Orthovoltage X-ray therapy can be considered as a treatment choice for local nasal lymphoma. X-ray therapy is a widely used modality in veterinary medicine considering the price of machines and costs of treatment.

Among the available technologies for treating natural and wastewater from clay materials, coagulation/flocculation is the most common method due to its high efficiency, simplicity, and cost-effectiveness. Inorganic coagulants such as aluminum sulfate and ferric chloride, widely used as destabilizing agents for colloidal particles, have several significant drawbacks: low efficiency and toxicity. Organic reagents of both natural and synthetic origin are a good alternative. This work is devoted to the evaluation of the flocculation action of new reagents, which are low molecular weight polymers based on amino ester salts on clay suspensions, as well as the selection of their optimal concentration, providing the maximum sedimentation rate. Studies have shown that amino ester salts can be effectively used for the treatment of water-clay suspensions. An important factor is the nature of the anion used, which has a significant influence on the oagulation ability of esters. Thus, 40–50 % (wt.) aqueous solutions of amino ester chlorides added to clay suspensions in an amount not exceeding 0.1% (vol.) can be used to thicken clay suspensions. At the same time, aqueous solutions of amino ester bromides regardless of the concentration, introduced into bentonite suspensions of 0.1–0.4 % (vol.), contribute to improved sedimentation, reducing viscosity, and increasing filtration capacity. These results allow us to recommend the use of amino ester chlorides as a thickener in the preparation of drilling muds for strengthening the walls of wells during drilling, and bromides – for flocculation of bentonite suspensions in oil production

The study presents an assessment of variability of histological structure, measurement, and comparison of size of the neoplasm obtained by ultrasonographic examination and pathological examination, as well as the morphometric dimensions of nuclei and cytoplasm of testicular interstitial cell tumors in dogs. The study involved 35 dogs with neoplasms of 46 testes, where 11 animals had interstitial cell tumors in both testes. Insignificant differences of the size of these neoplasms were revealed (p 0.05) using ultrasonography and pathoanatomical measurement methods. Hence, it allows using both methods to assess the size of interstitial cell tumors. In the study, interstitial cell tumor was detected in both testes at once in 50 % of cases in dogs, however, this might be due to specific characteristics of the sample, and further research is required. In the course of scientific work, a morphological study showed the presence of variability in histological structure of interstitial cell tumors, which can lead to incorrect interpretation of the morphological picture and misdiagnosis, e. g. adipocyte-like morphology of interstitial cell tumors have morphological similarity to a benign neoplasm from adipose tissue - lipoma. In addition, there was an extremely pronounced difference in size of cytoplasm (from 23.6 to 148.4 m; average 66.21 22.42 m) and nuclei (from 9 to 57.6 m; average 23.19 7.10 m) in tumor cells. It proves the presence of pronounced anisocytosis and anisokariosis, which should indicate malignancy of the neoplasm, however, testicular interstitial cell tumors extremely rarely metastasize in practice and according to numerous studies.

Background and Aim: Canine testicular tumors are among the most common reproductive tract tumors in male dogs and have been studied in many countries. However, to the best of our knowledge, studies with a large sample size have not been conducted in Russia. This study aimed to provide the latest information on the prevalence of canine testicular tumors in the Veterinary Oncology Scientific Center for Small Animals "Biocontrol" in Moscow, Russia, in 2010-2020 and the characteristics of the affected canine population. Materials and Methods: A retrospective review of patients and histological reports was collected and analyzed from 358 dogs with 447 testicular tumors within 11 years. Results: The mean age of the affected dogs was 10.4 years, whereas that of dogs with Sertoli cell tumors was 9.4 years p=0.009. This study includes mixed-breed dogs (18.4%), Yorkshire Terriers (8.8%), Labrador Retrievers (7.9%), Golden Retrievers (5.0%), and Fox Terriers (3.4%). The most common tumors were interstitial cell tumors (n=227, 50.8%). In contrast, 107 (23.9%) seminomas, 80 (17.9%) Sertoli cell tumors, 19 (7.4%) mixed germ cell-sex cord-stromal tumors, and 26 (7.6%) testicular tumors developed from cryptorchid testes, which included 16 (61.5%) Sertoli cell tumors, 10 (38.5%) seminomas, and no interstitial cell tumors. Conclusion: This study provides baseline information on the prevalence of canine testicular tumors in the described population, including the median age of each tumor type and overrepresented dog breeds. We further found that the most common scrotal testicular tumor was interstitial cell tumor, whereas Sertoli cell tumor was the most common in cryptorchid testicles.

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

Objective: Liver neoplasms are problematic among small domestic animals. The etiological cause of hepatocellular carcinomas in domestic animals is still unknown although it is believed that chronic infections and toxic substances can affect the development of this type of tumor. This study aimed to analyze the clinical and morphological characteristics of canine hepatocellular carcinoma. Materials and methods: In total, 6,958 cancer operations were performed in the clinic. Liver tumors were detected in 123 dogs in vivo and 375 dogs postmortem. All animals with suspected liver neoplasm were assessed, including history, clinical examination, complete blood count, biochemical blood tests, radiographic examination, and ultrasound with a biopsy for performing cytological and histological analyses. Results: Hepatocellular carcinomas have nonspecific clinical manifestations, also a characteristic aspect of other tumors of the hepatobiliary system. The hematological changes have an impact on the prognosis, and biochemical abnormalities reflect the changes in liver activity. The cytological diagnosis of hepatocellular tumors is difficult because of hepatocyte atypia in highly differenti¬ated carcinomas. Finally, a histological examination was performed in all the dogs diagnosed with hepatocellular carcinoma. Conclusion: Hematological changes in dogs with hepatocellular carcinoma affect their prognosis. Biochemical abnormalities of this pathology reflect the changes in liver activity, not indicating a specific pathology. However, an increase in the activity of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase is an unfavorable prognostic sign. In this study, five of seven dogs with a tumor size of more than 5.0 cm had a life expectancy of 30, 51, and 91 days, suggesting that the size of the tumor is an adverse prognostic factor. [J Adv Vet Anim Res 2020; 7(1.000): 127-132]

The TRIM37 (also known as MUL) gene is located in the 17q23 chromosomal region, which is amplified in up to ∼ 40% of breast cancers. TRIM37 contains a RING finger domain, a hallmark of E3 ubiquitin ligases, but its protein substrate(s) is unknown. Here we report that TRIM37 mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. We find that in human breast cancer cell lines containing amplified 17q23, TRIM37 is upregulated and, reciprocally, the major H2A ubiquitin ligase RNF2 (also known as RING1B) is downregulated. Genome-wide chromatin immunoprecipitation (ChIP)-chip experiments in 17q23-amplified breast cancer cells identified many genes, including multiple tumour suppressors, whose promoters were bound by TRIM37 and enriched for ubiquitinated H2A. However, unlike RNF2, which is a subunit of polycomb repressive complex 1 (PRC1), we find that TRIM37 associates with polycomb repressive complex 2 (PRC2). TRIM37, PRC2 and PRC1 are co-bound to specific target genes, resulting in their transcriptional silencing. RNA-interference-mediated knockdown of TRIM37 results in loss of ubiquitinated H2A, dissociation of PRC1 and PRC2 from target promoters, and transcriptional reactivation of silenced genes. Knockdown of TRIM37 in human breast cancer cells containing amplified 17q23 substantially decreases tumour growth in mouse xenografts. Conversely, ectopic expression of TRIM37 renders non-transformed cells tumorigenic. Collectively, our results reveal TRIM37 as an oncogenic H2A ubiquitin ligase that is overexpressed in a subset of breast cancers and promotes transformation by facilitating silencing of tumour suppressors and other genes.

Immunochromatographic tests (ICT) are diagnostics tools providing rapid results without the need for specialized equipment. Our aim was to evaluate retrospectively the rotavirus and adenovirus ICT routinely used in the virology laboratory serving the University Hospital of Marseille, France. From January 2017 to March 2020, 715 stool specimens from patients were screened using the Ridaquick Rotavirus/Adenovirus Combi ICT (RR/AC ICT) and a commercially available multiplex PCR detection kit. Rotavirus was detected in 9.2% of specimens by PCR and 7.7% of specimens by RR/AC ICT while adenovirus was detected in 8.5% of specimens by PCR and 2.4% of specimens by RR/AC ICT. The RR/AC ICT parameters for rotavirus were 75.8% sensitivity, 99.2% specificity, 90.9% positive predictive value (PPV) and 97.6% negative predictive value (NPV). The RR/AC ICT parameters for adenovirus were 6.6% sensitivity, 98.0% specificity, 23.5% PPV and 91.8% NPV. While the ICT test may be suitable for rotavirus detection, a PCR–based assay is better adapted for adenovirus detection in stools.

Cytomegalovirus (CMV) reactivations represent a significant morbidity and mortality problem in transplant patients. Reliable and rapid measurement of CMV viral load is a key issue for optimal patient management. We report here the evaluation of NeuMoDx™ (Qiagen) in a routine hospital setting (University Hospitals of Marseille, France) in comparison with our classical reference technique R-GENE. During one month, 719 CMV viral loads from 507 patients were measured in parallel in both techniques. Using the ROC (receiver operating characteristic) curve and our biological experience we suggest that values 140 IU/mL (Fowlkes–Mallows index) correspond to quantifiable positive results and values ranging from 52 to 140 IU/mL represent non-quantifiable positive results. Follow-up of 15 transplant patients who developed CMV reactivation during the study showed that NeuMoDx™ provided higher viral load measurement during the first two weeks of follow-up for three patients. These important intra-individual variations resulted in a significant median increase considering the whole data set (6.7 points of difference expressed as a percentage of the initial viral load). However, no difference between the two techniques was noticeable after two weeks of treatment. Subsequent to this first study we conclude that NeuMoDx™, used with optimized logistics and an adapted threshold, allows a rapid CMV viral load measurement and that its use does not lead to any difference in patient management compared to the reference technique R-GENE®.

Cytidine deaminase (CDA) deficiency leads to genome instability. Here the authors find a synthetic lethal interaction between CDA and the microtubule-associated protein Tau deficiencies, and report that Tau depletion affects rRNA synthesis, ribonucleotide pool balance, and rDNA stability.

BACKGROUND:In October 2010, Haiti was struck by a large-scale cholera epidemic. The Haitian government, UNICEF and other international partners launched an unprecedented nationwide alert-response strategy in July 2013. Coordinated NGOs recruited local rapid response mobile teams to conduct case-area targeted interventions (CATIs), including education sessions, household decontamination by chlorine spraying, and distribution of chlorine tablets. An innovative red-orange-green alert system was also established to monitor the epidemic at the communal scale on a weekly basis. Our study aimed to describe and evaluate the exhaustiveness, intensity and quality of the CATIs in response to cholera alerts in Haiti between July 2013 and June 2017. METHODOLOGY/PRINCIPAL FINDINGS:We analyzed the response to 7,856 weekly cholera alerts using routine surveillance data and severity criteria, which was based on the details of 31,306 notified CATIs. The odds of CATI response during the same week (exhaustiveness) and the number of complete CATIs in responded alerts (intensity and quality) were estimated using multivariate generalized linear mixed models and several covariates. CATIs were carried out significantly more often in response to red alerts (adjusted odds ratio (aOR) [95%-confidence interval, 95%-CI], 2.52 [2.22-2.87]) compared with orange alerts. Significantly more complete CATIs were carried out in response to red alerts compared with orange alerts (adjusted incidence ratio (aIR), 1.85 [1.73-1.99]). Over the course of the eight-semester study, we observed a significant improvement in the exhaustiveness (aOR, 1.43 [1.38-1.48] per semester) as well as the intensity and quality (aIR, 1.23 [1.2-1.25] per semester) of CATI responses, independently of funds available for the strategy. The odds of launching a CATI response significantly decreased with increased rainfall (aOR, 0.99 [0.97-1] per each accumulated cm). Response interventions were significantly heterogeneous between NGOs, communes and departments. CONCLUSIONS/SIGNIFICANCE:The implementation of a nationwide case-area targeted rapid response strategy to control cholera in Haiti was feasible albeit with certain obstacles. Such feedback from the field and ongoing impact studies will be very informative for actors and international donors involved in cholera control and elimination in Haiti and in other affected countries.

This article considers the problem of diagnosing local area network, as well as the task of structural determination is the creation and easy adjustment of the model object by building the knowledge base of available expert information. The algorithm of formalization of knowledge in designing intelligent systems is reviewed and proposed. The article considers the theory of fuzzy sets and fuzzy logic. The concept of the theory of fuzzy sets and fuzzy logic are formalized in the form of fuzzy and linguistic variables, and the vagueness of certain operations in the overall decision-making process is synthesized in the form of fuzzy algorithms. For the effective solution of tasks of type analysis and hypothetical sources of network problems in a local area network, a method of constructing membership functions based on analytical processing of the results of expert surveys is used.

Enteroviruses (EVs) are viruses of the family Picornaviridae that cause mild to severe infections in humans and in several animal species, including non-human primates (NHPs). We conducted a survey and characterization of enteroviruses circulating between humans and great apes in the Congo. Fecal samples (N = 24) of gorillas and chimpanzees living close to or distant from humans in three Congolese parks were collected, as well as from healthy humans (N = 38) living around and within these parks. Enteroviruses were detected in 29.4% of gorilla and 13.15% of human feces, including wild and human-habituated gorillas, local humans and eco-guards. Two identical strains were isolated from two humans coming from two remote regions. Their genomes were similar and all genes showed their close similarity to coxsackieviruses, except for the 3C, 3D and 5′-UTR regions, where they were most similar to poliovirus 1 and 2, suggesting recombination. Recombination events were found between these strains, poliovirus 1 and 2 and EV-C99. It is possible that the same EV-C species circulated in both humans and apes in different regions in the Congo, which must be confirmed in other investigations. In addition, other studies are needed to further investigate the circulation and genetic diversity of enteroviruses in the great ape population, to draw a definitive conclusion on the different species and types of enteroviruses circulating in the Republic of Congo.

O estado nutricional de 290 crianças, desde o nascimento até a idade de uns seis anos, da população Yanomami do Médio Rio Negro, Amazonas, foi observado em 1998 e 1999. Essa população tem um modo de viver tradicional e dispõe de um largo espaço para as atividades de caça e de colheita. O índice peso/altura foi comparado aos valores de referência do National Center for Health Statistics. Todas essas crianças são de pequena morfologia. Uma desnutrição (índice

Enterovirus A71 (EV-A71) has recently become an important public health threat, especially in South-East Asia, where it has caused massive outbreaks of Hand, Foot and Mouth disease every year, resulting in significant mortality. Rapid detection of EV-A71 early in outbreaks would facilitate implementation of prevention and control measures to limit spread. Real-time RT-PCR is the technique of choice for the rapid diagnosis of EV-A71 infection and several systems have been developed to detect circulating strains. Although eight genogroups have been described globally, none of these PCR techniques detect all eight. We describe, for the first time, a SYBR Green real-time RT-PCR system validated to detect all 8 EV-A71 genogroups. This tool could permit the early detection and shift in genogroup circulation and the standardization of HFMD virological diagnosis, facilitating networking of laboratories working on EV-A71 in different regions.

A presença da tuberculose no alto rio Negro (Brasil) é reportada desde o início deste século. Um inquérito retrospectivo desde 1977 e 1990 dos registros dos casos de tuberculose de duas estruturas sanitárias mostrou 699 casos, refletindo taxa de incidência anual muito elevada, superior a dois por mil habitantes, predominância das formas pulmonares, bem como distribuição da doença em todas as classes de idade. Os dados sobre a observância do tratamento ambulatório não são confiáveis. No contexto atual de degradação ambiental e de deterioração das condições sócio-econômicas dos índios, pode-se temer uma agravação da situação da tuberculose nesta região. O controle desta doença pode ser melhorado mediante intervenções sobre as condições de vida dos índios, e também sobre as atividades das estruturas de saúde.

A presença da tuberculose no alto rio Negro (Brasil) é reportada desde o início deste século. Um inquérito retrospectivo desde 1977 e 1990 dos registros dos casos de tuberculose de duas estruturas sanitárias mostrou 699 casos, refletindo taxa de incidência anual muito elevada, superior a dois por mil habitantes, predominância das formas pulmonares, bem como distribuição da doença em todas as classes de idade. Os dados sobre a observância do tratamento ambulatório não são confiáveis. No contexto atual de degradação ambiental e de deterioração das condições sócio-econômicas dos índios, pode-se temer uma agravação da situação da tuberculose nesta região. O controle desta doença pode ser melhorado mediante intervenções sobre as condições de vida dos índios, e também sobre as atividades das estruturas de saúde.The presence of tuberculosis in the upper Rio Negro region (Brazil) dates to the early 20th century. A retrospective survey of medical records in two clinics (one from 1977 and the other from 1990) showed 699 cases, with an extremely high annual incidence rate of over two per thousand, predominantly pulmonary cases, and distribution of the disease among all age groups. Data on compliance with outpatient treatment are not reliable. In the present context of deteriorating environmental and socioeconomic conditions among Indians, tuberculosis incidence may increase. Control of this disease could be enhanced by improving living conditions and health services for indigenous peoples.

ObjectivesWe characterized two new CTX-M-type extended-spectrum β-lactamase (ESBL) variants in Escherichia coli isolates from stool samples of two elderly patients admitted at the Tel Aviv Sourasky Medical Center, Israel. Both patients underwent treatment with cephalosporins prior to isolation of the E. coli strains.MethodsESBLs were detected by the double-disk synergy test and PCR-sequencing of β-lactamase genes. The bla(CTX-M) genes were cloned into the pCR-BluntII-TOPO vector in E. coli TOP10. The role of amino-acid substitutions V77A and D240G was analyzed by site-directed mutagenesis of the bla(CTX-M-94) and bla(CTX-M-100) genes and comparative characterization of the resulting E. coli recombinants. MICs of β-lactams were determined by Etest. Plasmid profiling, mating experiments, replicon typing and sequencing of bla(CTX-M) flanking regions were performed to identify the genetic background of the new CTX-M variants.ResultsThe novel CTX-M β-lactamases, CTX-M-94 and -100, belonged to the CTX-M-25-group. Both variants differed from CTX-M-25 by the substitution V77A, and from CTX-M-39 by D240G. CTX-M-94 differed from all CTX-M-25-group enzymes by the substitution F119L. Glycine-240 was associated with reduced susceptibility to ceftazidime and leucine-119 with increased resistance to ceftriaxone. bla(CTX-M-94) and bla(CTX-M-100) were located within ISEcp1 transposition units inserted into ∼93 kb non-conjugative IncFI and ∼130 kb conjugative IncA/C plasmids, respectively. The plasmids carried also different class 1 integrons.ConclusionsThis is the first report on CTX-M-94 and -100 ESBLs, novel members of the CTX-M-25-group.

Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways, and represent potential vulnerabilities that can be therapeutically exploited. Here we describe an RNA interference (RNAi)-based synthetic interaction screen to identify genes preferentially required for proliferation of p53-deficient (p53-) human cancer cells. We find that compared to p53-competent (p53+) human cancer cell lines, diverse p53- human cancer cell lines are preferentially sensitive to loss of the transcription factor ETV1 and the DNA damage kinase ATR. In p53- cells, RNAi-mediated knockdown of ETV1 or ATR results in decreased expression of the telomerase catalytic subunit TERT leading to growth arrest, which can be reversed by ectopic TERT expression. Chromatin immunoprecipitation analysis reveals that ETV1 binds to a region downstream of the TERT transcriptional start-site in p53- but not p53+ cells. We find that the role of ATR is to phosphorylate and thereby stabilize ETV1. Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53- cancer cells.

Real-time PCR techniques are now commonly used for the detection of viral genomes in various human specimens and require for validation both external and internal controls (ECs and ICs). In particular, ICs added to clinical samples are necessary to monitor the extraction, reverse transcription, and amplification steps in order to detect false-negative results resulting from PCR-inhibition or errors in the technical procedure. Here, we performed a large scale evaluation of the use of bacteriophages as ICs in routine molecular diagnosis. This allowed to propose simple standardized procedures (i) to design specific ECs for both DNA and RNA viruses and (ii) to use T4 (DNA) or MS2 (RNA) phages as ICs in routine diagnosis. Various technical formats for using phages as ICs were optimised and validated. Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. The frequency of inefficient detection of ICs was analyzed according to the nature of the sample. Inhibitors of enzymatic reactions were detected at high frequency in specific sample types such as heparinized blood and bone marrow (>70%), broncho-alveolar liquid (41%) and stools (36%). The use of T4 and MS2 phages as ICs proved to be cost-effective, flexible and adaptable to various technical procedures of real-time PCR detection in virology. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids.

BACKGROUND: In April 2009, the first cases of pandemic (H1N1)-2009 influenza [H1N1sw] virus were detected in France. Virological surveillance was undertaken in reference laboratories of the seven French Defence Zones. METHODOLOGY/PRINCIPAL FINDINGS: We report results of virological analyses performed in the Public Hospitals of Marseille during the first months of the outbreak. (i) Nasal swabs were tested using rapid influenza diagnostic test (RIDT) and two RT-PCR assays. Epidemiological characteristics of the 99 first suspected cases were analyzed, including detection of influenza virus and 18 other respiratory viruses. During three months, a total of 1,815 patients were tested (including 236 patients infected H1N1sw virus) and distribution in age groups and results of RIDT were analyzed. (ii) 600 sera received before April 2009 and randomly selected from in-patients were tested by a standard hemagglutination inhibition assay for antibody to the novel H1N1sw virus. (iii) One early (May 2009) and one late (July 2009) viral isolates were characterized by sequencing the complete hemagglutinine and neuraminidase genes. (iiii) Epidemiological characteristics of a cluster of cases that occurred in July 2009 in a summer camp were analyzed. CONCLUSIONS/SIGNIFICANCE: This study presents new virological and epidemiological data regarding infection by the pandemic A/H1N1 virus in Europe. Distribution in age groups was found to be similar to that previously reported for seasonal H1N1. The first seroprevalence data made available for a European population suggest a previous exposure of individuals over 40 years old to influenza viruses antigenically related to the pandemic (H1N1)-2009 virus. Genomic analysis indicates that strains harbouring a new amino-acid pattern in the neuraminidase gene appeared secondarily and tended to supplant the first strains. Finally, in contrast with previous reports, our data support the use of RIDT for the detection of infection in children, especially in the context of the investigation of grouped cases.

Within months of the emergence of the novel A/H1N1 pandemic influenza virus (nA/H1N1v), systematic screening for the surveillance of the pandemic was abandoned in France and in some other countries. At the end of June 2009, we implemented, for the public hospitals of Marseille, a Point Of Care (POC) strategy for rapid diagnosis of the novel A/H1N1 influenza virus, in order to maintain local surveillance and to evaluate locally the kinetics of the pandemic.Two POC laboratories, located in strategic places, were organized to receive and test samples 24 h/24. POC strategy consisted of receiving and processing naso-pharyngeal specimens in preparation for the rapid influenza diagnostic test (RIDT) and real-time RT-PCR assay (rtRT-PCR). This strategy had the theoretical capacity of processing up to 36 samples per 24 h. When the flow of samples was too high, the rtRT-PCR test was abandoned in the POC laboratories and transferred to the core virology laboratory. Confirmatory diagnosis was performed in the core virology laboratory twice a day using two distinct rtRT-PCR techniques that detect either influenza A virus or nA/N1N1v. Over a period of three months, 1974 samples were received in the POC laboratories, of which 111 were positive for nA/H1N1v. Specificity and sensitivity of RIDT were 100%, and 57.7% respectively. Positive results obtained using RIDT were transmitted to clinical practitioners in less than 2 hours. POC processed rtRT-PCR results were available within 7 hours, and rtRT-PCR confirmation within 24 hours.The POC strategy is of benefit, in all cases (with or without rtRT-PCR assay), because it provides continuous reception/processing of samples and reduction of the time to provide consolidated results to the clinical practitioners. We believe that implementation of the POC strategy for the largest number of suspect cases may improve the quality of patient care and our knowledge of the epidemiology of the pandemic.

Abstract Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenome, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database.

O Sertão de Pernambuco não é área endêmica nem focal para esquistossomose mansônica. O presente trabalho registra a ocorrência de Biomphalaria straminea em açude da região, constatando que suas águas têm características físico-químicas favoráveis à proliferação destes moluscos. Chama a atenção para a possibilidade da introdução da doença no semi-árido, diante da crescente multiplicação de barragens.

The article deals with the organization of project-based education applied in the supplementary higher vocational education system and considers the needs of modern society in the context of creating a Priority Development Area. (PDA). In the article, the authors present the architecture of the integrated model of traditional and project-based learning in the supplementary vocational education system, offer practical recommendations on the organization and implementation of project activities in the staff training demanded in PDA. The article reflects the results of introducing the integrated model of traditional and project-based learning in the supplementary vocational education system. [ABSTRACT FROM AUTHOR]